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<div class="title">moltk/EString.hpp</div>  </div>
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<a href="EString_8hpp.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*</span>
<a name="l00002"></a>00002 <span class="comment">    MolTK is a Python and C++ toolkit for protein sequence/structure alignment and visualization</span>
<a name="l00003"></a>00003 <span class="comment">    Copyright (C) 2011  Christopher M. Bruns</span>
<a name="l00004"></a>00004 <span class="comment"></span>
<a name="l00005"></a>00005 <span class="comment">    This program is free software; you can redistribute it and/or modify</span>
<a name="l00006"></a>00006 <span class="comment">    it under the terms of the GNU General Public License as published by</span>
<a name="l00007"></a>00007 <span class="comment">    the Free Software Foundation; either version 2 of the License, or</span>
<a name="l00008"></a>00008 <span class="comment">    (at your option) any later version.</span>
<a name="l00009"></a>00009 <span class="comment"></span>
<a name="l00010"></a>00010 <span class="comment">    This program is distributed in the hope that it will be useful,</span>
<a name="l00011"></a>00011 <span class="comment">    but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00012"></a>00012 <span class="comment">    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
<a name="l00013"></a>00013 <span class="comment">    GNU General Public License for more details.</span>
<a name="l00014"></a>00014 <span class="comment"></span>
<a name="l00015"></a>00015 <span class="comment">    You should have received a copy of the GNU General Public License along</span>
<a name="l00016"></a>00016 <span class="comment">    with this program; if not, write to the Free Software Foundation, Inc.,</span>
<a name="l00017"></a>00017 <span class="comment">    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</span>
<a name="l00018"></a>00018 <span class="comment">    </span>
<a name="l00019"></a>00019 <span class="comment">    Commercial users should ask about our dual licensing model.</span>
<a name="l00020"></a>00020 <span class="comment">    For questions contact: cmbruns@rotatingpenguin.com</span>
<a name="l00021"></a>00021 <span class="comment">*/</span>
<a name="l00022"></a>00022 
<a name="l00029"></a>00029 <span class="preprocessor">#ifndef MOLTK_ESTRING_HPP</span>
<a name="l00030"></a>00030 <span class="preprocessor"></span><span class="preprocessor">#define MOLTK_ESTRING_HPP</span>
<a name="l00031"></a>00031 <span class="preprocessor"></span>
<a name="l00032"></a>00032 <span class="preprocessor">#include &lt;iostream&gt;</span>
<a name="l00033"></a>00033 <span class="preprocessor">#include &lt;vector&gt;</span>
<a name="l00034"></a>00034 
<a name="l00035"></a>00035 <span class="keyword">namespace </span>moltk {
<a name="l00036"></a>00036 
<a name="l00038"></a><a class="code" href="classmoltk_1_1EString.html">00038</a> <span class="keyword">class </span><a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a>
<a name="l00039"></a>00039 {
<a name="l00040"></a>00040 <span class="keyword">public</span>:
<a name="l00041"></a>00041 
<a name="l00050"></a><a class="code" href="classmoltk_1_1EString_1_1const__iterator.html">00050</a>     <span class="keyword">class </span><a class="code" href="classmoltk_1_1EString_1_1const__iterator.html" title="Iterator for accessing the residue positions encoded in an estring.">const_iterator</a>
<a name="l00051"></a>00051     {
<a name="l00052"></a>00052     <span class="keyword">public</span>:
<a name="l00053"></a><a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#a01ca7c5f3f2ebebee963d591ba185353">00053</a>         <a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#a01ca7c5f3f2ebebee963d591ba185353">const_iterator</a>() {}
<a name="l00054"></a>00054         <a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#a01ca7c5f3f2ebebee963d591ba185353">const_iterator</a>(<span class="keyword">const</span> std::vector&lt;int&gt;&amp; <a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#a3491024e82a7e6604138b9821cd61cac">runs</a>
<a name="l00055"></a>00055                 , <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#a4023b95df1ce183cabeea986e0f3e4a0">run_index</a>
<a name="l00056"></a>00056                 , <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#a9997888176246e21da82d252d96638a7">position_index</a>);
<a name="l00057"></a>00057         <a class="code" href="classmoltk_1_1EString_1_1const__iterator.html" title="Iterator for accessing the residue positions encoded in an estring.">const_iterator</a>&amp; <a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#a746264fc5967bfa98a658fa0a24a7606">operator++</a>();
<a name="l00058"></a>00058         <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#a32e99838282c1f8fd4b3813a41c2182c">operator*</a>() <span class="keyword">const</span> ;
<a name="l00059"></a>00059         <span class="keywordtype">bool</span> <a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#aae4b2d9ad56dba2f9bf869fbb0d05f41">operator!=</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1EString_1_1const__iterator.html" title="Iterator for accessing the residue positions encoded in an estring.">const_iterator</a>&amp; rhs);
<a name="l00060"></a>00060         <span class="keywordtype">bool</span> <a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#a9dc6a81765839885054aa681153a841a">operator==</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1EString_1_1const__iterator.html" title="Iterator for accessing the residue positions encoded in an estring.">const_iterator</a>&amp; rhs);
<a name="l00061"></a>00061 
<a name="l00062"></a>00062     <span class="keyword">protected</span>:
<a name="l00063"></a><a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#a3491024e82a7e6604138b9821cd61cac">00063</a>         <span class="keyword">const</span> std::vector&lt;int&gt;* <a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#a3491024e82a7e6604138b9821cd61cac">runs</a>;
<a name="l00064"></a><a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#a4023b95df1ce183cabeea986e0f3e4a0">00064</a>         <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#a4023b95df1ce183cabeea986e0f3e4a0">run_index</a>;
<a name="l00065"></a><a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#a9997888176246e21da82d252d96638a7">00065</a>         <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#a9997888176246e21da82d252d96638a7">position_index</a>;
<a name="l00066"></a><a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#aebfe683ee618731fb3548e2f6a6d16f4">00066</a>         <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1EString_1_1const__iterator.html#aebfe683ee618731fb3548e2f6a6d16f4">sequence_index</a>;
<a name="l00067"></a>00067     };
<a name="l00068"></a>00068 
<a name="l00069"></a>00069 
<a name="l00070"></a>00070     <a class="code" href="classmoltk_1_1EString.html#ad5c5f1ca824e409441a132595727516a">EString</a>();
<a name="l00071"></a>00071     <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a> <a class="code" href="classmoltk_1_1EString.html#ae5141544f2f35fd6e7dc52e433cf840d">operator*</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a>&amp; rhs) <span class="keyword">const</span>;
<a name="l00072"></a>00072     <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a>&amp; <a class="code" href="classmoltk_1_1EString.html#aef861c7800f5665af4af9eab4a791795">append_run</a>(<span class="keywordtype">int</span> run);
<a name="l00073"></a><a class="code" href="classmoltk_1_1EString.html#aeb89cc399d87b5ebe50ee41bae4024bd">00073</a>     <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a>&amp; <a class="code" href="classmoltk_1_1EString.html#aeb89cc399d87b5ebe50ee41bae4024bd">operator&lt;&lt;</a>(<span class="keywordtype">int</span> run) {<a class="code" href="classmoltk_1_1EString.html#aef861c7800f5665af4af9eab4a791795">append_run</a>(run); <span class="keywordflow">return</span> *<span class="keyword">this</span>;}
<a name="l00074"></a>00074     <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1EString.html#abccf52caeb356f6ed7e9f34aaa14c7e3">ungapped_length</a>() <span class="keyword">const</span>;
<a name="l00075"></a>00075     <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1EString.html#a7c4543e6d5c1a7d467bd91f4b22e95a3">total_length</a>() <span class="keyword">const</span>;
<a name="l00076"></a>00076     const_iterator <a class="code" href="classmoltk_1_1EString.html#ab86a2dae75151c1e8bd542e052c7b6ff">begin</a>() <span class="keyword">const</span>;
<a name="l00077"></a>00077     const_iterator <a class="code" href="classmoltk_1_1EString.html#abfc1fa93f66f077a932107cc3faabaf9">end</a>() <span class="keyword">const</span>;
<a name="l00078"></a>00078     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1EString.html#a586773d72e57fe5a86ecaf3ae61aeabc">reverse</a>();
<a name="l00079"></a><a class="code" href="classmoltk_1_1EString.html#a805c088cf32ad2fb4ab0ad28b10e876c">00079</a>     <span class="keywordtype">bool</span> <a class="code" href="classmoltk_1_1EString.html#a805c088cf32ad2fb4ab0ad28b10e876c">operator==</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a>&amp; rhs)<span class="keyword"> const </span>{ <span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1EString.html#a3569a7942663b16e4294bcd5ddbb25cc">runs</a> == rhs.<a class="code" href="classmoltk_1_1EString.html#a3569a7942663b16e4294bcd5ddbb25cc">runs</a>; }
<a name="l00080"></a><a class="code" href="classmoltk_1_1EString.html#a3cc39e881687891eed0af5fa1e33d90c">00080</a>     <span class="keywordtype">bool</span> <a class="code" href="classmoltk_1_1EString.html#a3cc39e881687891eed0af5fa1e33d90c">operator!=</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a>&amp; rhs)<span class="keyword"> const </span>{ <span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1EString.html#a3569a7942663b16e4294bcd5ddbb25cc">runs</a> != rhs.<a class="code" href="classmoltk_1_1EString.html#a3569a7942663b16e4294bcd5ddbb25cc">runs</a>; }
<a name="l00081"></a><a class="code" href="classmoltk_1_1EString.html#ae4f1df70ed9a50bfbd573defd2c90d49">00081</a>     <span class="keyword">inline</span> <span class="keyword">friend</span> std::ostream&amp; <a class="code" href="classmoltk_1_1EString.html#aeb89cc399d87b5ebe50ee41bae4024bd">operator&lt;&lt;</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a>&amp; e)
<a name="l00082"></a>00082     {
<a name="l00083"></a>00083         os &lt;&lt; <span class="stringliteral">&quot;&lt;&quot;</span>;
<a name="l00084"></a>00084         std::vector&lt;int&gt;::const_iterator i;
<a name="l00085"></a>00085         <span class="keywordflow">for</span> (i = e.<a class="code" href="classmoltk_1_1EString.html#a3569a7942663b16e4294bcd5ddbb25cc">runs</a>.begin(); i != e.<a class="code" href="classmoltk_1_1EString.html#a3569a7942663b16e4294bcd5ddbb25cc">runs</a>.end(); ++i) 
<a name="l00086"></a>00086         {
<a name="l00087"></a>00087             <span class="keywordflow">if</span> (i != e.<a class="code" href="classmoltk_1_1EString.html#a3569a7942663b16e4294bcd5ddbb25cc">runs</a>.begin()) os &lt;&lt; <span class="stringliteral">&quot;, &quot;</span>;
<a name="l00088"></a>00088             os &lt;&lt; *i;
<a name="l00089"></a>00089         }
<a name="l00090"></a>00090         os &lt;&lt; <span class="stringliteral">&quot;&gt;&quot;</span>;
<a name="l00091"></a>00091         <span class="keywordflow">return</span> os;
<a name="l00092"></a>00092     }
<a name="l00093"></a>00093 
<a name="l00094"></a>00094 <span class="keyword">protected</span>:
<a name="l00095"></a><a class="code" href="classmoltk_1_1EString.html#a3569a7942663b16e4294bcd5ddbb25cc">00095</a>     std::vector&lt;int&gt; <a class="code" href="classmoltk_1_1EString.html#a3569a7942663b16e4294bcd5ddbb25cc">runs</a>;
<a name="l00096"></a><a class="code" href="classmoltk_1_1EString.html#af930d7290e6b6a0be911a194069c2cfa">00096</a>     <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1EString.html#af930d7290e6b6a0be911a194069c2cfa">m_ungapped_length</a>;
<a name="l00097"></a><a class="code" href="classmoltk_1_1EString.html#a2900d588fd81ac22258b3039dc367a62">00097</a>     <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1EString.html#a2900d588fd81ac22258b3039dc367a62">m_total_length</a>;
<a name="l00098"></a>00098 };
<a name="l00099"></a>00099 
<a name="l00100"></a>00100 } <span class="comment">// namespace moltk</span>
<a name="l00101"></a>00101 
<a name="l00102"></a>00102 
<a name="l00103"></a>00103 <span class="preprocessor">#endif // MOLTK_ESTRING_HPP</span>
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